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Hereditary Sensory Neuropathy Type IA via the SPTLC1 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
SPTLC1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9861SPTLC181479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Angela Gruber, PhD

Clinical Features and Genetics

Clinical Features

Hereditary Sensory Neuropathy Type IA (HSN1A) is an axonal form of Charcot-Marie-Tooth neuropathy (hereditary motor and sensory neuropathy) (Nicholson et al. 2015. PubMed ID: 20301563). Patients with this disorder manifest prominent sensory loss, “burning” and “shooting” pains (Rotthier et al. 2011. PubMed ID: 21618344). The loss of sensation may lead to painless injuries, which, if unheeded, could result in osteomyelitis and require distal amputations (Rotthier et al. 2009. PubMed ID: 19651702; Auer-Grumbach et al. 2013. PubMed ID: 23454272; Nicholson et al. 2015. PubMed ID: 20301563). Motor involvement is usually observed in advanced cases and patients may become wheelchair-bound in their 60s or 70s (Auer-Grumbach et al. 2013. PubMed ID: 23454272). The disease onset is highly variable (Nicholson et al. 2015. PubMed ID: 20301563).


HSN1A is inherited in an autosomal dominant (AD) manner, and incomplete penetrance has been reported (Houlden et al. 2006. PubMed ID: 16364956; Nicholson et al. 2015. PubMed ID: 20301563). This disorder is caused by pathogenic variants in the SPTLC1 (serine palmitoyltransferase, long chain base subunit 1) gene, which encodes an enzyme involved in sphingolipid biosynthesis (Bejaoui et al. 2001. PubMed ID: 11242106; Dawkins et al. 2001. PubMed ID: 11242114). To date, only missense variant in this gene has been reported to cause disease (Human Gene Mutation Database). Pathogenic variants in the active sites of SPTLC1 lead to a gain-of-function by altering substrate specificity and producing toxic sphingolipids. The accumulation of neurotoxic lipids 1-deoxy-sphinganine and 1-deoxymethyl-sphinganine has been observed in the plasma of patients with HSN1A (Penno et al. 2010. PubMed ID: 20097765).

Clinical Sensitivity - Sequencing with CNV PGxome

It is difficult to estimate the exact clinical sensitivity of this test due to the lack of large cohort studies. All the pathogenic variants in the SPTLC1 gene reported to date can be detected by sequencing.

Testing Strategy

This test provides full coverage of all coding exons of the SPTLC1 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Patients with symptoms consistent with AD sensory and motor neuropathy may consider this test.


Official Gene Symbol OMIM ID
SPTLC1 605712
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Auer-Grumbach et al. 2013. PubMed ID: 23454272
  • Bejaoui et al. 2001. PubMed ID: 11242106
  • Dawkins et al. 2001. PubMed ID: 11242114
  • Houlden et al. 2006. PubMed ID: 16364956
  • Human Gene Mutation Database (Bio-base).
  • Nicholson et al. 2015. PubMed ID: 20301564
  • Penno et al. 2010. PubMed ID: 20097765
  • Rotthier et al. 2009. PubMed ID: 19651702
  • Rotthier et al. 2011. PubMed ID: 21618344


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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